Inter-array similarity calculated on the Arabidopsis dataset normalized by RMA, GCRMA and MAS5. 1000 groups of arrays for each sample size were selected, and then the averages and standard deviations of inter-array Spearman correlation coefficients were calculated. The averages are reproduced as symbols which are connected by a broken line and averages plus minus one standard deviation are shown as shaded areas bordered by a solid line of the same color. Values for MAS5 are shown in red, RMA in blue and GCRMA in green. A) real samples. B) samples with their raw signal intensities internally permutated.